Table 1.

Species-specific peptide identification and SRM method building

	Discovery phase		Validation phase			SRM method
			Experimental DDA analysis		In silico
	Number of strains used for peptide identification	Number of identified peptides	Number of strains used as negative control	Specific and inclusive peptidesa	Specific peptides against all Uniprot taxonomies (BLAST)	Number of targeted specific peptidesb
E. coli	29	14,107	93d	288	70c	24
A. baumannii	10	8049	104e	562	52	16
S. pneumoniae	7	7408	140f	85	44	11
P. aeruginosa	10	5999	121g	5397	304	20
H. influenzae	10	7456	122h	5321	520	10
S. aureus	13	6043	99i	1283	282	15

^aSpecificity was validated for peptides not identified in negative control strains; inclusiveness was validated for peptides identified in 70% of the targeted strains

^bInteresting peptides were selected among the specific one (previous column), regarding their amino-acid sequence and MS sensitivity

^cE. coli or Shigella-specific peptides

^dA. baumannii, E. aerogenes, E. cloacae, H. influenzae, K. oxytoca, K. pneumoniae, P. mirabilis, P. aeruginosa, S. marcescens, S. aureus, S. pneumoniae

^eA. calcoaceticus, A. haemolyticus, A. junii, E. aerogenes, E. cloacae, E. coli, H. influenzae, K. oxytocca, K. pneumoniae, P. mirabilis, P. aeruginosa, S. marcescens, S. aureus, S. pneumoniae

^fA. baumannii, E. cloacae, E. aerogenes, E. coli, H. influenzae, K. oxytoca, K. pneumoniae, P. mirabilis, P. aeruginosa, S. marcescens, S. aureus, S. agalactiae, S. anginosus, S. constellatus, S. infantis, S. intermedius, S. mitis, S. mutans, S. oralis, S. pseudopneumoniae, S. pyogenes, S. salivarius, S. sanguinis

^gA. baumannii, E. cloacae, E. aerogenes, E. coli, H. influenzae, K. oxytoca, K. pneumoniae, P. mirabilis, P. alcaligenes, P. putida, P. stutzeri, S. marcescens, S. aureus, S. pneumoniae

^hA. baumannii, E. cloacae, E. aerogenes, E. coli, H. haemolyticus, H. parainfluenzae, K. pneumoniae, K. oxytoca, P. mirabilis, P. aeruginosa, S. marcescens, S. aureus, S. pneumoniae

ⁱA. baumannii, E. cloacae, E. aerogenes, E. coli, H. influenzae, K. oxytoca, K. pneumoniae, P. mirabilis, P. aeruginosa, S. marcescens, S. haemolyticus, S. warneri, S. epidermidis, S. pneumoniae